Variant report

Variant	rs11897712
Chromosome Location	chr2:99735697-99735698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10179043	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10190421	0.85[CEU][hapmap]
rs12053372	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12468807	0.84[CEU][hapmap]
rs12474833	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12475034	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12477438	0.84[EUR][1000 genomes]
rs1349778	0.85[CEU][hapmap]
rs1349779	0.85[CEU][hapmap]
rs1453561	0.85[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs1453562	0.85[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs1563107	0.85[CEU][hapmap]
rs1563108	0.85[CEU][hapmap]
rs1580068	0.85[CEU][hapmap]
rs17708218	0.85[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs17760953	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1922624	1.00[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs1968916	0.81[EUR][1000 genomes]
rs1993230	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2045057	0.85[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2309524	0.85[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs3851334	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324365	0.85[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs4851184	0.85[CEU][hapmap]
rs4851196	0.81[EUR][1000 genomes]
rs58206803	1.00[ASN][1000 genomes]
rs60012524	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153764	0.85[EUR][1000 genomes]
rs62156364	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6542873	0.85[EUR][1000 genomes]
rs6704766	0.85[CEU][hapmap]
rs6754843	0.80[CEU][hapmap]
rs6756880	0.80[CEU][hapmap]
rs6757019	0.85[CEU][hapmap]
rs896886	0.85[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs9308816	0.85[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs972768	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9808541	0.85[CEU][hapmap]
rs995617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11897712	TSGA10	cis	multi-tissue	Pritchard
rs11897712	TSGA10	cis	parietal	SCAN
rs11897712	FAM178B	cis	cerebellum	SCAN
rs11897712	FAHD2B	cis	parietal	SCAN
rs11897712	LIPT1	cis	cerebellum	SCAN
rs11897712	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs11897712	ZAP70	cis	parietal	SCAN
rs11897712	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11897712	LIPT1	cis	parietal	SCAN
rs11897712	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs11897712	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99718000-99740200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:99718600-99739600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:99723800-99739600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:99729400-99741600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:99732400-99738000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:99735600-99741400	Weak transcription	Brain Angular Gyrus	brain

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